Pluripotent stem cells, which include induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs), are characterized by a capacity for self-renewal and an ability to differentiate into any functional cell in the body. Thus, pluripotent stem cells are valuable sources of differentiated somatic cell types for research and clinical applications. The advent of human iPSCs (hiPSCs), derived from somatic cells by the exogenous expression of defined transcription factors, has overcome ethical issues associated with human ESCs (hESCs) and, when derived from the patient, may avoid immunological complications. While promising, significant limitations to the therapeutic use of hiPSCs remain unresolved. These include interline variations ranging from inconsistent transcription factor expression and differential DNA methylation to sporadic point mutations and chromosomal defects that affect in vitro differentiation, tumorigenicity, and potential clinical applications (Lee et al., Nature Med. 19(8): p. 998-1004 (2013); Robinton and Daley, Nature 481:295-305 (2012); Feng et al., Stem Cells 28:704-712 (2010); Gore et al., Nature 471:63-67 (2011)). Moreover, current tests of hiPSC potency rely on extensive in vitro differentiation tests, in vivo teratoma assays in rodents (Robinton and Daley, Nature 481, 295-305 (2012); Maherali and Hochedlinger, Cell Stem Cell 3:595-605 (2008)) or bioinformatic and gene expression assays (Bock et al., Cell 144:439-452 (2011); Muller et al., Nat. Methods 8:315-317 (2011)) which cannot be practically implemented into high-throughput hiPSC line generation designed to limit interline variability.